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Manganese in PDB 2dti: Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+)

Enzymatic activity of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+)

All present enzymatic activity of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+):
6.3.4.15;

Protein crystallography data

The structure of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+), PDB code: 2dti was solved by B.Bagautdinov, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.54 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.351, 82.628, 72.718, 90.00, 102.22, 90.00
R / Rfree (%) 23.4 / 28.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+) (pdb code 2dti). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+), PDB code: 2dti:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2dti

Go back to Manganese Binding Sites List in 2dti
Manganese binding site 1 out of 2 in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1501

b:24.9
occ:1.00
 OP1 B:BT51301 2.0 23.7 1.0
O1 A:POP1401 2.1 30.4 1.0
O5 A:POP1401 2.2 25.5 1.0
OD2 A:ASP104 2.3 21.1 1.0
OD1 A:ASP104 2.4 21.8 1.0
OD1 A:ASN103 2.6 19.4 1.0
CG A:ASP104 2.7 22.3 1.0
P1 A:POP1401 3.2 33.4 1.0
O A:POP1401 3.2 31.5 1.0
P2 A:POP1401 3.3 30.0 1.0
CG A:ASN103 3.3 23.0 1.0
NZ A:LYS111 3.4 36.0 1.0
ND2 A:ASN103 3.5 20.2 1.0
P B:BT51301 3.5 29.4 1.0
O5' B:BT51301 4.0 28.0 1.0
O2 A:POP1401 4.1 32.9 1.0
O3 A:POP1401 4.2 29.1 1.0
CB A:ASP104 4.2 21.4 1.0
O6 A:POP1401 4.2 27.6 1.0
OP2 B:BT51301 4.2 23.9 1.0
OCB B:BT51301 4.3 27.8 1.0
O4 A:POP1401 4.4 31.8 1.0
NZ A:LYS100 4.4 23.7 1.0
CD A:ARG48 4.5 28.7 1.0
NH1 A:ARG51 4.5 31.1 1.0
NH1 A:ARG48 4.5 27.1 1.0
OBB B:BT51301 4.5 27.8 1.0
C A:ASN103 4.6 23.8 1.0
CE A:LYS111 4.6 36.0 1.0
O A:ASN103 4.7 24.8 1.0
CB A:ASN103 4.7 23.1 1.0
N A:ASP104 4.8 22.4 1.0
CBB B:BT51301 4.8 28.8 1.0
N A:ASN103 4.8 26.2 1.0
CD A:PRO102 4.8 28.9 1.0
CA A:ASN103 5.0 24.6 1.0
CA A:ASP104 5.0 21.9 1.0

Manganese binding site 2 out of 2 in 2dti

Go back to Manganese Binding Sites List in 2dti
Manganese binding site 2 out of 2 in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mn(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1502

b:47.5
occ:1.00
 O6 B:POP1402 2.2 40.1 0.5
OD2 B:ASP104 2.2 25.0 1.0
OP1 B:BT51302 2.3 34.2 1.0
OD1 B:ASP104 2.5 25.5 1.0
OD1 B:ASN103 2.7 27.4 1.0
CG B:ASP104 2.7 25.1 1.0
O4 B:POP1402 2.7 30.8 0.5
O2 B:POP1402 2.9 37.3 0.5
O4 B:POP1402 3.0 41.5 0.5
O B:POP1402 3.0 34.8 0.5
P2 B:POP1402 3.1 39.2 0.5
P1 B:POP1402 3.4 35.2 0.5
P2 B:POP1402 3.4 31.4 0.5
CG B:ASN103 3.5 28.8 1.0
ND2 B:ASN103 3.7 28.9 1.0
NZ B:LYS111 3.8 30.9 1.0
P B:BT51302 3.8 33.5 1.0
O B:POP1402 4.0 39.8 0.5
O3 B:POP1402 4.1 34.5 0.5
O6 B:POP1402 4.2 29.9 0.5
O5' B:BT51302 4.2 32.8 1.0
CB B:ASP104 4.2 26.0 1.0
O5 B:POP1402 4.2 40.1 0.5
NZ B:LYS100 4.2 24.9 1.0
OCB B:BT51302 4.3 33.2 1.0
O B:HOH1566 4.3 33.4 1.0
CD B:ARG48 4.4 36.6 1.0
OP2 B:BT51302 4.5 35.6 1.0
CE B:LYS111 4.6 33.0 1.0
OBB B:BT51302 4.7 34.3 1.0
N B:ASP104 4.8 24.5 1.0
CD B:PRO102 4.8 31.0 1.0
O5 B:POP1402 4.8 32.5 0.5
O1 B:POP1402 4.8 37.3 0.5
C B:ASN103 4.8 25.8 1.0
CB B:ASN103 4.9 28.0 1.0
N B:ASN103 4.9 30.5 1.0
NH1 B:ARG48 4.9 38.9 1.0
CBB B:BT51302 4.9 33.3 1.0

Reference:

B.Bagautdinov, N.Kunishima. Ligand Structures of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Sat Oct 5 13:46:49 2024

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